Hi Jado54, If you suspect you have malware you can run a full system scan whilst in Safe mode by pressing F8 quickly just before windows loads then running TDS3 with all scan options enabled.
In normal mode NOD will be the first to show an alert when TDS3 opens a file to scan if NOD already has definitions for a particular Trojan.
If you enable TDS3'S Execution Protection then Trojans will not be allowed to run.
Remember that Execution Protection is only active if TDS3 is showing it's GUI or is iconised in the systray.

In other words if one does not catch it the other will - TDS3, NOD32 work well together.

Sorry but I would like to clarify as the posts are a bit contradictory
Is it best only to scan in safe mode or does it not really matter? I may run my scans just because I am paranoid but not because I necessarily suspect already anything. If I can do that without deactivating other programs knowing it will not create conflicts, I would prefer to do it that way.

Running TDS3 in safe mode can allow it to remove malware that may have been running in normal mode. This is the same for many types of scanners as quite often the scanner cannot disable the process to remove it or else needs to reboot your machine to complete the task.
Also if you have a resident Anti-vitus scanner it may jump in as TDS opens the file and this too could stop TDS from being able to remove it.
You can, of course, use TDS3 in normal user mode for scanning files etc. and any malware found will be reported.
Running Execution Protection will stop any identified malware from running.